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Expression data from paired matched breast cancer Fine needle aspiration (FNA) or Core needle biopsies (CBX)

ABSTRACT: Paired FNA and CBX specimens were prospectively collected from 37 breast cancers before any systemic therapy during a biomarker discovery study at The University of Texas M. D. Anderson Cancer Center. We identified 293 probe sets overexpressed in core biopsies; these included five highly coexpressed gene clusters (metagenes) corresponding to immune functions and extracellular matrix components. We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes Pre-treatment paird matched FNA and CBX from primary tumors were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

ORGANISM(S): Homo sapiens

SUBMITTER: TAKAYUKI IWAMOTO 

PROVIDER: E-GEOD-32518 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Molecular anatomy of breast cancer stroma and its prognostic value in estrogen receptor-positive and -negative cancers.

Bianchini Giampaolo G   Qi Yuan Y   Alvarez Ricardo H RH   Iwamoto Takayuki T   Coutant Charles C   Ibrahim Nuhad K NK   Valero Vicente V   Cristofanilli Massimo M   Green Marjorie C MC   Radvanyi Laszlo L   Hatzis Christos C   Hortobagyi Gabriel N GN   Andre Fabrice F   Gianni Luca L   Symmans W Fraser WF   Pusztai Lajos L  

Journal of clinical oncology : official journal of the American Society of Clinical Oncology 20100830 28

<h4>Purpose</h4>The purpose of this study was to identify genes enriched in breast cancer stroma, assess the stromal gene expression differences between estrogen receptor (ER) -positive and -negative cancers, and separately determine their prognostic value in these two subtypes of breast cancers.<h4>Methods</h4>We compared gene expression profiles of pairs of fine-needle (stroma-poor) and core-needle (stroma-rich) biopsies from 37 cancers to identify stroma-associated genes. We defined stromal m  ...[more]

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